Mechanism of Organophosphonate Catabolism by Diiron Oxygenase PhnZ: A Third Iron-Mediated O–O Activation Scenario in Nature

Diiron oxygenase PhnZ catalyzes the catabolism of organophosphonate (Pn) (<i>R</i>)-2-amino-1-hydroxyethylphosphonic to glycine and inorganic phosphate (Pi). In this Pn catabolism way, PhnZ oxidatively cleaves the highly stable C–P bond in Pn to produce Pi. However, the mechanism of this enzyme that affords aquatic and marine bacteria in Pi-limited environments to utilize the most abundant environmental Pn (2-amino-ethylphosphonic acid) as the source of Pi is still unclear. In this work, extensive QM/MM calculations reveal that the mechanism of PhnZ consists of four consecutive steps: (1) rate-limiting α-H abstraction of Pn by Fe^III-superoxo; (2) formation of Fe^IIIOOC_α peroxide; (3) concerted O insertion into C_α–P bond of Pn initiated by “inverse” heterolytic O–O cleavage; and (4) phosphate hydrolysis to glycine and Pi. Intriguingly, the enzymatic reaction mechanism of PhnZ for the crucial breakage of the C–P bond is characterized by the “inverse” heterolytic O–O cleavage of Fe^IIIOOC_α intermediate, which renders the distal O atom more oxidative to oxygenate Pn than the homolytic O–O cleavage. In this way, PhnZ adopts a mechanism quite different from the related diiron oxygenase MIOX, with His62 residue playing an important role. This unusual “inverse” heterolytic O–O cleavage mode, apart from the well-known homolytic and “normal” heterolytic ones, constitutes a third iron-mediated O–O activation scenario in nature, which is expected to have its broad occurrence in oxidative transformation involving heteroatoms of sulfur and phosphorus

Shapeshifting Nucleophile Singly Hydrated Hydroperoxide Anion Leads to the Occurrence of the Thermodynamically Unfavored S_N2 Product

Single water molecules alone may introduce unusual features into the kinetics and dynamics of chemical reactions. The singly hydrated hydroperoxide anion, HOO–(H2O), was found to be a shapeshifting nucleophile, which can be transformed to HO– solvated by hydrogen peroxide HO–(HOOH). Herein, we performed direct dynamics simulations of its reaction with methyl iodide to investigate the effect of individual water molecules. In addition to the normal SN2 product CH3OOH, the thermodynamically unfavored proton transfer-induced HO–-SN2 path (produces CH3OH) was also observed, contributing ∼4%. The simulated branching ratio of the HO–-SN2 path exceeded the statistical estimation (0.6%) based on the free energy barrier difference. The occurrence of the HO–-SN2 path was attributed to the shallow entrance channel well before a submerged saddle point, thus providing a region for extensive proton exchange and ultimately leading to the formation of CH3OH. In comparison, changing the leaving group from Cl to I increased the overall reaction rate as well as the proportion of the HO–-SN2 path because the CH3I system has a smaller internal barrier. This work elucidates the importance of the dynamic effect introduced by a single solvent molecule to alter the product channel and kinetics of typical ion–molecule SN2 reactions

Shapeshifting Nucleophile Singly Hydrated Hydroperoxide Anion Leads to the Occurrence of the Thermodynamically Unfavored S_N2 Product

Single water molecules alone may introduce unusual features into the kinetics and dynamics of chemical reactions. The singly hydrated hydroperoxide anion, HOO–(H2O), was found to be a shapeshifting nucleophile, which can be transformed to HO– solvated by hydrogen peroxide HO–(HOOH). Herein, we performed direct dynamics simulations of its reaction with methyl iodide to investigate the effect of individual water molecules. In addition to the normal SN2 product CH3OOH, the thermodynamically unfavored proton transfer-induced HO–-SN2 path (produces CH3OH) was also observed, contributing ∼4%. The simulated branching ratio of the HO–-SN2 path exceeded the statistical estimation (0.6%) based on the free energy barrier difference. The occurrence of the HO–-SN2 path was attributed to the shallow entrance channel well before a submerged saddle point, thus providing a region for extensive proton exchange and ultimately leading to the formation of CH3OH. In comparison, changing the leaving group from Cl to I increased the overall reaction rate as well as the proportion of the HO–-SN2 path because the CH3I system has a smaller internal barrier. This work elucidates the importance of the dynamic effect introduced by a single solvent molecule to alter the product channel and kinetics of typical ion–molecule SN2 reactions

Calculated Mechanism of Cyanobacterial Aldehyde-Deformylating Oxygenase: Asymmetric Aldehyde Activation by a Symmetric Diiron Cofactor

Cyanobacterial aldehyde-deformylating oxygenase (cADO) is a nonheme diiron enzyme that catalyzes the conversion of aldehyde to alk­(a/e)­ne, an important transformation in biofuel research. In this work, we report a highly desired computational study for probing the mechanism of cADO. By combining our QM/MM results with the available ⁵⁷Fe Mössbauer spectroscopic data, the gained detailed structural information suggests construction of asymmetry from the symmetric diiron cofactor in an aldehyde substrate and O₂ activation. His₁₆₀, one of the two iron-coordinate histidine residues in cADO, plays a pivotal role in this asymmetric aldehyde activation process by unprecedented reversible dissociation from the diiron cofactor, a behavior unknown in any other nonheme dinuclear or mononuclear enzymes. The revealed intrinsically asymmetric interactions of the substrate/O₂ with the symmetric cofactor in cADO are inspirational for exploring diiron subsite resolution in other nonheme diiron enzymes

Thermal Methane Conversion to Syngas Mediated by Rh₁‑Doped Aluminum Oxide Cluster Cations RhAl₃O₄⁺

Laser ablation generated RhAl₃O₄⁺ heteronuclear metal oxide cluster cations have been mass-selected using a quadrupole mass filter and reacted with CH₄ or CD₄ in a linear ion trap reactor under thermal collision conditions. The reactions have been characterized by state-of-the-art mass spectrometry and quantum chemistry calculations. The RhAl₃O₄⁺ cluster can activate four C–H bonds of a methane molecule and convert methane to syngas, an important intermediate product in methane conversion to value-added chemicals. The Rh atom is the active site for activation of the C–H bonds of methane. The high electron-withdrawing capability of Rh atom is the driving force to promote the conversion of methane to syngas. The polarity of Rh oxidation state is changed from positive to negative after the reaction. This study has provided the first example of methane conversion to syngas by heteronuclear metal oxide clusters under thermal collision conditions. Furthermore, the molecular level origin has been revealed for the condensed-phase experimental observation that trace amounts of Rh can promote the participation of lattice oxygen of chemically very inert support (Al₂O₃) to oxidize methane to carbon monoxide

DataSheet_1_Pectin methylesterase 31 is transcriptionally repressed by ABI5 to negatively regulate ABA-mediated inhibition of seed germination.docx

Pectin methylesterase (PME), a family of enzymes that catalyze the demethylation of pectin, influences seed germination. Phytohormone abscisic acid (ABA) inhibits seed germination. However, little is known about the function of PMEs in response to ABA-mediated seed germination. In this study, we found the role of PME31 in response to ABA-mediated inhibition of seed germination. The expression of PME31 is prominent in the embryo and is repressed by ABA treatment. Phenotype analysis showed that disruption of PME31 increases ABA-mediated inhibition of seed germination, whereas overexpression of PME31 attenuates this effect. Further study found that ABI5, an ABA signaling bZIP transcription factor, is identified as an upstream regulator of PME31. Genetic analysis showed that PME31 functions downstream of ABI5 in ABA-mediated seed germination. Detailed studies showed that ABI5 directly binds to the PME31 promoter and inhibits its expression. In the plants, PME31 expression is reduced by ABI5 in ABA-mediated seed germination. Taken together, PME31 is transcriptionally inhibited by ABI5 and negatively regulates ABA-mediated seed germination inhibition. These findings shed new light on the mechanisms of PMEs in response to ABA-mediated seed germination.</p